Tagged with #haploid unifed_genotyper snps
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Created 2013-02-22 02:15:18 | Updated | Tags: unifiedgenotyper
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I trying to detect variants in a population of haploid genomes with UnifiedGenotyper, using the -sample_ploidy option to specify the number of haploid genomes in the pool. I would like to be able to specify other options, but so far the ones I have tried do not seem to work. I have tried: -out_mode EMIT_ALL_SITES --sample_ploidy 50 -minIndelFrac 0.05 --genotype_likelihoods_model BOTH -pnrm EXACT_GENERAL_PLOIDY. Could you please tell me which, if any, of the other commands are available when calling variants on non-diploid samples? Specifically, I would really like to be able to call indels too.

Thanks for your time and help.


Created 2012-10-26 20:18:35 | Updated 2012-10-26 20:37:27 | Tags:
Comments (1)

Is there a new argument to replace '--multiallelic' . I am trying to determine all valid alternative alleles for a single position even if the call is the same as the reference. Both the sample(s) and the reference are haploid bacterial genomes.